chr1-29792805-T-C

Variant names:

• chr1-29792805-T-C
• rs6691847

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.848 in 152,082 control chromosomes in the GnomAD database, including 54,865 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.85 (54865 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.417
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.848 AC: 128858 AN: 151964 Hom.: 54823 Cov.: 31

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.922

Gnomad EAS AF: 0.789

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.870

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.848 AC: 128951 AN: 152082 Hom.: 54865 Cov.: 31 AF XY: 0.843 AC XY: 62634 AN XY: 74326

African (AFR) AF: 0.791 AC: 32810 AN: 41464

American (AMR) AF: 0.822 AC: 12562 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.922 AC: 3201 AN: 3470

East Asian (EAS) AF: 0.789 AC: 4061 AN: 5150

South Asian (SAS) AF: 0.887 AC: 4283 AN: 4826

European-Finnish (FIN) AF: 0.799 AC: 8448 AN: 10572

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.892 AC: 60672 AN: 68000

Other (OTH) AF: 0.871 AC: 1838 AN: 2110

Alfa AF: 0.878 Hom.: 259546

Bravo AF: 0.847

Asia WGS AF: 0.860 AC: 2992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.40
PhyloP100		-0.42

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6691847; hg19: chr1-30265652;